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New QFC Publication on Estimating Effective Sample Sizes in Assessment Models


Sam Truesdell (QFC Post-Doctoral Research Associate), Jim Bence (QFC Co-Director), John Syslo (QFC Post-Doctoral Research Associate), and Mark Ebener (Chippewa-Ottawa Resource Authority) recently had a paper accepted for publication in Fisheries Research for a special issue on data weighting in stock assessment models. These results have previously been shared with members of the Modeling Subcommittee for 1836 Treaty Waters, and the methodology is the basis for a planned workshop at Michigan State University in December 2016.

Integrated stock assessment models use data from multiple sources. For example, in catch-at-age models both the annual landed fish weight and the proportion of fish in each age class (measured via scientific sampling) are considered together. Catch-at-age models evaluate the trends in these data simultaneously, but some data sources are better indicators of population trajectories than others. Part of developing stock assessment models is assigning levels of certainty to each data source (i.e., a weight). This can be particularly difficult for the proportion-at-age samples (termed composition data). Common methods for assigning assessment model weights to fishery compositions typically do not account for processes often seen in the analysis of fishery data, such as that fish with similar characteristics (e.g., of similar ages) are often caught together, leading to correlations in the composition data. This means that composition data are often less informative then they appear based on the number of fish sampled and aged. This can lead to inflated composition weights that can produce biased estimates of population characteristics (such as stock size) and may lead to sub-optimal management strategies. Truesdell and co-authors survey methods for estimating the optimum weight for composition data (the effective sample size) in stock assessment models and apply them to two Great Lakes fish stocks – one in Lake Michigan and one in Lake Huron. They also introduces a new method that can account for correlations in composition data using a statistical approach.

The in-press article can be found here. The citation for the article and the abstract is below.


Truesdell, S.B., J.R. Bence, J.M. Syslo, and M.P. Ebener. In press. Estimating multinomial effective sample size in catch-at-age and catch-at-size models. Fisheries Research
Abstract.-Catch-at-age or catch-at-size stock assessment models require specification of an effective sample size (ESS) as a weighting component for multinomial composition data. ESS weights these data relative to other data that are fit, and is not an estimable parameter within a model that uses a multinomial likelihood. The ESS is typically less than the actual sample size (the number of fish) because of factors such as sampling groups of fish (clusters) that are caught together. A common approach for specifying ESS is to iteratively re-fit the model, estimating ESS after each fit so that the standardized residual variance is “correct,” until ESS converges. We survey iterative methods for determining ESS for a multinomial likelihood and apply them to two Great Lakes whitefish stocks. We also propose an extension of such methods: (the Generalized Mean Approach – GMA) for the case where ESS is based on mean age (or length) to account for correlation structures among proportions. Our extension allows for greater flexibility in the relationship between ESS and sampling intensity. Our results show that the choice of ESS estimation method can impact assessment model results. Simulations (in the absence of correlation structures) showed that all the approaches to calculating effective sample size could provide reasonable results on average, however methods that estimated annual ESS independently across years were highly imprecise. In our simulations and application, methods that did account for correlation structure in annual proportions produced lower ESS than those that did not and suggested that these methods are adjusting for a deviation from the multinomial correlation structure. We recommend using methods that adjust for correlation structures in the proportions, and either assuming a constant ESS or, when there is substantial inter-annual variation in sampling levels, assuming ESS is related to sampling intensity and using the GMA or a similar approach to estimate that relationship.

New QFC Publication Exploring the Consequences of Stock Assessment Frequency


Yang Li (QFC PhD student), Jim Bence (QFC Co-Director), and Travis Brenden (QFC Associate Director) recently published a paper in North American Journal of Fisheries Management exploring the consequences of moving from annual to less-frequent assessment of fish stocks. Annually assessing fish stocks can be difficult and time consuming; consequently, agencies are often interested in moving away from annual assessments. As part of their research, they evaluated how assessment frequency affected fishery management outcomes and how outcomes were affected by factors such as data quality, variability in population recruitment, and harvest level. They additionally evaluated methods for setting target harvest levels in years between assessments when assessments were not conducted annually.

The published article can be found here. The full citation for the published article and the abstract is below.


Li, Y., J.R. Bence, and T.O. Brenden. 2016. The influence of stock assessment frequency on achievement of fishery management objectives. North American Journal of Fisheries Management 36:793-812.
Abstract.-Because of resource limitations with respect to both funding and staff expertise, there is growing interest among fishery management agencies in moving from annual to less-frequent assessments of fish stocks. We conducted simulations based on Lake Whitefish populations in the Laurentian Great Lakes to evaluate (1) how statistical catch-at-age assessment frequency, the time lag between data collection and assessment, and approaches to setting target harvests in the years between assessments affected the achievement of management objectives; and (2) how the outcomes were influenced by the quality of assessment data, features of the populations, and characteristics of the fisheries exploiting the populations. We found that as assessments became less frequent, relative yields were reduced and the risk of stock depletion and interannual variation in yield increased. The effects of less-frequent assessments were ameliorated in populations with greater levels of productivity and when target mortality was lower. Conversely, the effects of assessment frequency were largely insensitive to changes in recruitment variation or the quality of assessment data.

Science Transfer Workshop – S.D.M. Process for Barrier Removal Decisions


As part of the Great Lakes Fishery Commission’s Science Transfer Program, members of the QFC will hold two, two-day workshops during November 14-17, 2016. The first workshop will take place in Detroit, MI, and the second in Toronto, ON. Intended for Great Lakes fisheries managers, each workshop will consist of a mock Structured Decision Making (SDM) process for barrier removal decisions, presentations by experts on the state of science in predicting native and invasive fish production above barriers, and guided discussion on research and decision-making. Workshop participants will learn the methods of SDM and gain an increased understanding of the scientific knowledge and uncertainty in predicting fish production above existing barriers.

If interested in attending, you can register for one of the workshops by providing your name, email address, and preferred workshop location to Alex Jensen at jense100@msu.edu, or inquire further about the workshops at the same address. Initial registration will be used to determine final workshop enrollment on a first-come, first-serve basis, as attendance is capped at 30 participants per workshop. There is no registration fee for these workshops

QFC heads to IAGLR 2016


The International Association for Great Lakes Research (IAGLR) holds its annual conference in Guelph Ontario, June 6-10 and the QFC will be attending in force. Co-Directors Bence and Jones, both former Presidents of IAGLR, will be attending, and Bence will be at the IAGLR board meeting and reporting for the Publication Committee. Dr. Dobiesz, QFC research scientist/scientific programmer, will be attending in her role as Technical Editor for the Journal of Great Lakes Research, and will be presenting the Editor’s Workshop entitled “Reviews: How to Give and Take”, providing guidance and background on the review process for authors and reviewers. Yang Li (PhD candidate) will be presenting a poster co-authored by Drs. Bence and Brenden in the “Biology and Ecology of Great Lakes Fish” session entitled “Bayesian variable selection for the determination of factors related to fish movement distance.” Alex Maguffee (MS student) will be presenting a talk titled “Differences in otolith chemistry of Lake Michigan Chinook Salmon to identify natal origin” co-authored by Drs. Jones, Clark, and Reilly in that same session. Lisa Peterson (PhD student) will be presenting a talk co-authored with Dr. Jones titled “Evaluating methods for estimating mortality of Great Lakes Walleye using acoustic telemetry in the “Using acoustics as a tool for ecosystem-based aquatic research and monitoring” session.

Reneé Reilly Returns to a Warmer Climate


Reneé Reilly, a QFC Post-Doctoral Research Associate since 2013, braved 3 Michigan winters but recently elected to return to Virginia to pursue a marketing position in the private sector. While at the QFC, Reneé worked on a variety of projects, including management strategy evaluation for Lake Erie percids, Minnesota Mille Lacs walleye assessment and management review, movement modeling of Chinook salmon between Lakes Michigan and Huron, and determining natal origins of Chinook salmon in Lake Michigan through otolith microchemistry. Reneé also served as the technical lead for the QFC’s Introduction to R online course and recently co-led the development of an R graphing short course. Reneé also enlivened the QFC’s social element and was always encouraging of a common lunch time, coffee break, or St. Patrick’s Day party. QFC staff and students wish Reneé all their best and hope she enjoys the warmer weather and her new career opportunity!

Dr. Kelly Robinson – New QFC Faculty Member


Dr. Kelly Robinson has joined the QFC and the MSU Department of Fisheries and Wildlife as an Assistant Professor. Kelly is originally from Chesapeake, VA, and attended the University of Virginia as an undergraduate, majoring in Biology and Spanish. She then received her M.S. in Marine Biology from the College of Charleston, where she studied age, growth and reproduction of barrelfish. Kelly received her Ph.D. in Fisheries Science from the University of Georgia. Her doctoral research focused on fish assemblages in managed wetlands in coastal South Carolina. She studied the productivity of fish guilds within these structures, compared resident fish assemblages in managed and unmanaged wetlands, and used structured decision making (SDM) to evaluate impoundment management strategies. This interest in SDM and decision analysis led Kelly to a Post-Doctoral appointment at Cornell University, where she worked with the New York State Department of Environmental Conservation to use SDM to evaluate harvest management strategies for white-tailed deer and wild turkey. While at Cornell, Kelly had the opportunity to work with other groups to implement SDM, including evaluating the effects of nest exclosures on piping plover populations with managers and biologists in the northeastern U.S. and two projects designed to aid managers and biologists in making the best decisions for mitigating the effects of climate change on the ecosystems of the San Francisco Bay Estuary. Kelly is excited to return to the aquatic environment to study the fisheries of Michigan and the Great Lakes and to use SDM to help the Great Lakes Fishery Commission and other stakeholders to make sound management decisions for fish populations in the Great Lakes and throughout Michigan.

QFC Participation in Fisheries & Wildlife Graduate Research Symposium


On February 26, the Department of Fisheries and Wildlife Graduate Student Organization (GSO) hosted its 11th Annual GSO Research Symposium. This year’s symposium, which consisted of oral presentations by Fisheries and Wildlife graduate students and poster presentations by undergraduate researchers, was financially supported in part by the QFC. At last year’s symposium, Matt Vincent, a QFC Ph.D. student, won the Best Fisheries Presentation Award. At this year’s symposium, 3 M.S. students (Nick Fisch, Alex Jensen, and Alex Maguffee) and 1 Ph.D. student (Lisa Peterson) from the QFC gave oral presentations. The titles of their presentations were the following:
Nick Fisch: “Quantitative Tools for Assessing and Managing Cisco Populations”
Alex Jensen: “Hierarchical Modeling of Larval Sea Lamprey Habitat”
Alex Maguffee: “Quantifying Differences in Otolith Chemistry of Chinook Salmon in Lake Michigan to Determine Natal Origins”
Lisa Peterson: “Evaluating Methods for Estimating Mortality of Great Lakes Walleye Using Acoustic Telemetry”
The Keynote Speaker for the symposium was Dr. Hillary Young, a community ecologist from the University of California-Santa Barbara.

QFC Teaches Trial Version of an R Graphing Workshop


At the beginning of January, the QFC taught a trial version of an R graphing workshop entitled “Unleashing the Power of R as a Graphing Tool”. The workshop was designed as an introduction to creating advanced and publishable graphics for those with a working knowledge of R. The material focused heavily on both basic and more complex features of the base package but also covered the fundamentals of more advanced packages such as ggplot2 and RColorBrewer, as well as an introduction to creating figures with spatial data. Information was shared through both lecture and simultaneous “live” coding in the R environment on a separate screen. Thirteen graduate students and post-doctoral research associates from the Department of Fisheries and Wildlife at MSU participated in the day-long workshop. Participants were asked to complete exercises to help them master the content, and were provided answer keys along with the sample code used during class at the end of the workshop. The QFC received useful feedback on what parts of the course were effective and how to improve future workshops. The developers of the workshop (Yang Li, Lisa Peterson, Reneé Reilly, Sam Truesdell, and Matt Vincent) will be working to refine the workshop itself and adapt material for an online course during spring 2016.
RGraphingCourse

Jones receives award from Ontario Commercial Fisheries Association


At their 2016 Annual Convention in Niagara Falls, Ontario, the Ontario Commercial Fisheries’ Association (OCFA) presented QFC Co-Director Dr. Michael Jones with the 2016 Robert J. Graham Partnership Award. This award recognizes efforts to promote partnerships and understanding among fishery stakeholders. The OCFA selected Mike for the award in recognition of his engagement with OCFA over his 25+ years as an OMNRF Research Scientist and Michigan State University Professor, and particularly for his leadership of the Lake Erie Percid Management Advisory Group (LEPMAG) process since 2010. “I am greatly honored to receive this award”, said Jones, “partly because of my fond memories of it’s namesake, Rob Graham, and also because LEPMAG has been among the most rewarding experiences of my professional career”. LEPMAG continues to provide guidance for Lake Erie fishery managers about walleye and yellow perch fisheries based on open discussions of the fishery assessment and harvest policies among a diverse and representative group of fishery stakeholders.

QFC Involvement at the Midwest Fish and Wildlife Conference

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The QFC is heavily involved in this year’s Midwest Fish and Wildlife Conference, which is being held at the Amway Grand Plaza Hotel in Grand Rapids, Michigan. The conference kicks off next week with workshops and a reception on Sunday January 24, followed by technical sessions Monday to Wednesday. The QFC’s Associate Director, Travis Brenden, is one of the program co-chairs for the conference. The QFC (along with MSU’s Quantitative Wildlife Center) is co-sponsoring a symposium on Monday entitled “State-Space Models for Fish and Wildlife Population Dynamics.” The QFC’s Reneé Riley will be moderating the symposium and Reneé and Brian Stevens were part of the team that organized it. The session will be kicked off by a keynote talk by Ken Newman from the USFWS. Both QFC co-Directors will be presenting at the conference. Mike Jones is giving an “IGNITE” talk, which is a relatively novel (for fisheries folk) format of 5 minutes for 20 slides that advance automatically every 15 seconds, with the provocative title of “Why don’t we just admit we have no idea what we’re doing?” Jim Bence will be giving a talk at the State-Space symposium that overviews the status of applications of state space modeling in fishery stock assessments. There will be a number of other QFC presentations including talks by Lori Ivan (Can vaccinated hatchery fish be used to prevent disease spread? A case study of VHS IVb), Rick Clark (Most Chinook salmon stocked into northern Lake Huron have been feeding in Lake Michigan since the collapse of alewives in Lake Huron), Bryan Stevens (Integrated assessment of harvested wild turkey populations in southern Michigan: a state-space approach), Alex Jensen (Hierarchical modeling of larval sea lamprey Petromyzon marinus habitat), Cleyo Harris (Tributary use and large-scale movement of grass carp: patterns to inform control efforts in western Lake Erie), Kelley Smith (Current state of Michigan crayfishes), and Travis Brenden (Indexing recruitment fluctuations for populations contributing to mixtures by simultaneous analysis of age and genetic information). Lisa Peterson will be moderating a session on percid fisheries and other QFC staff will be attending and volunteering in various capacities.